Contacts of the helix formed by residues 401 - 415 (chain A) in PDB entry 2WOK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A ALA 4.6 4.8 - - - +
338A ARG* 4.4 24.0 - - - +
399A ARG 4.2 0.6 + - - -
400A GLY* 1.3 69.2 - - - -
402A PHE* 1.3 68.1 + - + +
404A LEU* 3.2 14.7 + - + +
405A VAL* 3.1 27.5 + - - +
5B PHE* 5.7 7.2 - - + -
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Residues in contact with PHE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A HIS* 4.1 9.4 - + - -
338A ARG* 3.7 22.9 - - - -
397A THR* 2.8 23.3 + - - +
398A GLN* 3.5 31.0 - - + +
399A ARG 4.7 0.6 + - - +
400A GLY* 3.3 0.8 - - - -
401A LYS* 1.3 79.4 - - + +
403A ARG* 1.3 57.9 + - - +
405A VAL* 3.4 3.9 + - - +
406A ALA* 2.9 22.3 + - - +
430A TYR* 4.0 5.2 - + - -
431A PHE* 3.8 20.4 - + - -
450A VAL* 3.7 33.3 - - + +
451A THR* 3.8 3.4 - - - -
452A ASP* 3.8 31.9 - - + -
5B PHE* 3.6 29.1 - + - -
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Residues in contact with ARG 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A THR* 3.9 5.4 - - - -
398A GLN 3.1 18.2 + - - +
399A ARG* 4.0 0.4 - - - -
400A GLY 3.1 16.0 + - - +
402A PHE* 1.3 76.2 - - - +
404A LEU* 1.3 62.8 + - + +
406A ALA* 3.2 0.7 + - - +
407A ASP* 2.9 62.8 + - - +
422A VAL* 3.7 35.8 + - - +
424A GLU* 2.9 47.4 + - - +
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ALA* 3.5 32.1 - - + +
400A GLY 3.3 14.1 + - - +
401A LYS* 3.2 13.8 + - + +
403A ARG* 1.3 78.5 - - + +
405A VAL* 1.3 62.6 + - - +
407A ASP* 3.4 16.2 + - + +
408A ALA* 3.2 16.6 + - - +
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Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A HIS* 3.3 33.2 - - + +
307A VAL* 5.1 0.2 - - + -
334A LEU* 4.1 10.1 - - + +
337A ALA* 3.9 7.6 - - + -
338A ARG* 3.9 30.7 - - + +
401A LYS 3.1 14.8 + - - +
402A PHE 3.7 7.0 - - - +
404A LEU* 1.3 74.1 - - - +
406A ALA* 1.3 64.3 + - - +
408A ALA* 3.0 6.1 + - - +
409A VAL* 3.0 22.4 + - + +
450A VAL* 4.0 14.8 - - + -
526A LEU* 3.8 19.7 - - + -
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ILE* 4.1 27.9 - - + +
397A THR* 3.8 24.9 - - + -
402A PHE 2.9 15.2 + - - +
403A ARG 3.2 8.5 + - - +
405A VAL* 1.3 76.1 - - - +
407A ASP* 1.3 56.3 + - - +
409A VAL* 3.0 4.9 + - - +
410A VAL* 2.9 33.4 + - - +
422A VAL* 4.3 6.7 - - + -
450A VAL* 4.2 5.6 - - + +
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Residues in contact with ASP 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A ARG* 2.9 54.8 + - - +
404A LEU* 3.5 20.6 - - + +
406A ALA* 1.3 77.4 - - - +
408A ALA* 1.3 56.9 + - - +
410A VAL* 3.2 9.4 + - - +
411A GLU* 2.9 28.7 + - - +
422A VAL* 4.1 6.8 - - - +
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Residues in contact with ALA 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A LEU* 3.8 29.1 - - + +
334A LEU* 3.4 18.8 - - + -
337A ALA* 4.0 15.0 - - + -
404A LEU 3.2 11.3 + - - +
405A VAL 3.0 9.7 + - - +
407A ASP* 1.3 73.2 - - - +
409A VAL* 1.3 60.5 + - - +
411A GLU* 4.5 1.3 - - - -
412A SER* 2.9 33.3 + - - -
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Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A VAL* 4.3 17.9 - - + -
325A VAL* 5.5 1.8 - - + -
334A LEU* 3.6 19.3 - - + -
395A ILE* 3.9 22.2 - - + -
405A VAL* 3.0 22.2 + - + +
406A ALA 3.0 6.5 + - - +
408A ALA* 1.3 74.5 - - - +
410A VAL* 1.3 66.0 + - - +
412A SER* 3.2 4.9 + - - -
413A LEU* 3.0 40.7 + - + +
420A LEU* 3.7 19.5 - - + -
448A LEU* 4.7 7.0 - - + -
450A VAL* 5.1 0.2 - - + -
524A LEU* 6.0 4.5 - - + -
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A ILE* 4.5 0.7 - - + -
406A ALA 2.9 19.4 + - - +
407A ASP* 3.2 11.0 + - - +
409A VAL* 1.3 77.3 - - - +
411A GLU* 1.3 63.4 + - - +
413A LEU* 4.0 0.7 - - - +
414A ALA* 3.0 28.5 + - + +
418A ILE 4.7 1.4 - - - +
420A LEU* 3.9 45.5 + - + +
422A VAL* 3.7 26.5 - - + -
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A LEU* 3.7 29.8 - - + +
407A ASP 2.9 16.3 + - - +
408A ALA* 3.9 4.9 - - - +
410A VAL* 1.3 80.8 - - - +
412A SER* 1.3 63.5 + - - +
414A ALA* 3.6 11.8 + - - +
415A ARG* 3.6 15.7 - - + +
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Residues in contact with SER 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ALA* 3.4 25.1 - - - +
329A ALA* 4.2 4.7 - - - -
330A ASP* 3.1 30.8 + - - +
333A LEU* 4.2 2.8 - - - +
334A LEU* 4.5 3.4 - - - +
408A ALA 2.9 24.2 + - - -
409A VAL* 3.5 8.6 - - - -
411A GLU* 1.3 76.8 - - - +
413A LEU* 1.3 62.7 + - - +
415A ARG* 2.9 34.2 + - - +
416A VAL 4.6 0.2 + - - -
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A VAL* 3.8 46.7 - - + +
328A ALA* 3.7 28.3 - - + +
329A ALA* 4.6 1.3 - - - +
409A VAL* 3.0 39.3 + - + +
410A VAL 4.3 0.9 - - - +
412A SER* 1.3 76.3 - - - +
414A ALA* 1.3 66.0 + - - +
415A ARG 3.1 2.2 - - - -
416A VAL* 3.0 18.4 + - - +
418A ILE* 3.2 41.9 + - + +
420A LEU* 4.0 14.1 - - + -
448A LEU* 4.5 4.5 - - + -
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A VAL* 3.0 21.8 + - + +
411A GLU* 3.7 9.2 - - - +
413A LEU* 1.3 77.6 - - - +
415A ARG* 1.3 57.3 + - + +
417A GLY* 3.0 18.6 + - - +
418A ILE 3.4 12.7 + - - +
419A GLU* 5.5 1.6 - - - +
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Residues in contact with ARG 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ALA 2.8 28.1 + - - -
330A ASP* 3.7 19.3 + - - +
372A ARG* 2.8 34.3 + - - +
373A GLY* 3.9 0.8 + - - -
375A LEU* 3.7 40.1 - - + +
379A ARG* 3.2 20.6 + - - -
411A GLU* 3.6 12.6 - - + +
412A SER* 2.9 20.3 + - - +
414A ALA* 1.3 76.7 - - - +
416A VAL* 1.3 58.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il